Chuck versus The New Life
by dragonslayer9907
Summary: What if Chuck was extracted at the end of the first season, but instead of being locked up he was trained to be a super spy? Strong Chuck, Chuck&Sarah. Chapter 2 has a bit of new content.
1. Chuck versus the Desert Resort

Dragonslayer9907 signing in.  
Disclaimer: I don't own anything, because if I did I probably wouldn't be writing here.

Chuck versus The Desert Resort

"Sarah, can you tell everyone, Morgan, Ellie, Devon, that I that I love them and that if am supposed to be dead, can you find a way to make it easier for them?" Chuck said.

"Yeah, I can do that. Chuck, it was nice working with you." Sarah said.

"You know Sarah, this really isn't that bad. Now that I'm going to be confined, you and I can actually go on a real date. You can come over to my cell sometime and hang out and we can actually test out our feelings. Goodbye Sarah!" Chuck said.

Suddenly, a chopper landed on top of a roof in the middle of Burbank, California.

"We're here for the package! The Intersect is going to be extracted for his own protection. We need to extract him immediately." the agents on the chopper said as they took Chuck onto the chopper.

"Agent Walker, you and Major Casey are on standby until the Intersect is capable of surviving in the real world without your protection 24/7. This will only take a few months. His cover story is a business trip to China to help set up multiple stores. We'll see you later then" the agents ordered as they closed the doors of the chopper.  
The chopper flew for at least three hours before landing in the middle of nowhere in the Mojave Desert. The agents took Chuck to a door in the sand and took him into the underground base situated there. When Chuck walked into the underground base he was in for the shock of his life. The base was like a tropical resort, with a fake ocean, beach, fancy living quarters, and very, very lively parties.

"What is this place?" Chuck asked.

"Agent Carmichael, welcome to the B9907 operations base. This base is the place where our most valued assets and agents gather to be trained or train the newcomers. Everything you see is available for your use after your training is complete." the agents explained, "Come on we'll need to meet up with your new teachers and show you your room."

They walked through the beach to the living quarters before taking an elevator to the bottom of the B9907 operations base. They walked down a long narrow hallway to a metal door with a security pad next to it. One of the agents put his palm on the pad and the door opened and behind the door was something that blew Chuck's mind.

The room was a state of the art training room equipped with the newest anti-theft security measures and very very dangerous obstacles and weapons.( Imagine the X-men danger room except much more lethal and practical) There were two agents in the room going through the obstacles as if it were something they did every day.

"Agent Carmichael, your new teachers Agent Sigma and Agent X. Agent Sigma is a master at almost everything in the world. He is what most consider an Intersect, except he doesn't have the Intersect, because you do. And Agent X is the most lethal weapons master and trained ninja in our agency. Many of our agents were the pupils of Agent X in weaponry. Almost everyone in the agency has been taught by these two and they have helped many assets become agents." one agent said. "So Agent Carmichael are you ready for action?"

"Yes, yes I am," Chuck said as he looked at the two agents in awe.

"Oh and one more thing. When your training is done, they'll be joining your team." the agent said.

Chuck walked into the training room and the doors closed behind him, not to open for a very long time.

Six months later

Chuck was training in the training room finishing his last mastery of the double spears and getting the Intersect upgraded to the Intersect 2.0. With the new Intersect, Chuck was able to do things that most couldn't, such as learning Kung Fu in less than a second, even though he doesn't need to. Anyway, today is the last day of Chuck's containment in the B9907 underground operations base.

"Okay Chuck, your last test is going to be to see if you can break out of the B9907 base without any help. When you get out of the base we'll be waiting for you at the entrance with the chopper. You have twelve hours to get out and you aren't allowed to kill anyone not that you could anyway." Agent X said.

"You are only allowed no weapons use all that you have learned and the Intersect to get out of the base. Your test starts... NOW!" Agent Sigma said.

"Okay I got this." Chuck said.

Chuck ran up the stairs from the bottom of the base to the first floor. Chuck swiftly got rid of the security guards that were guarding the hallway clearing the first hallway. He jumped off the walls and kicked open the door to the stairway up to the second floor. When he got to the second floor, the agents surrounded the entrance to the hallway. Chuck picked a metal pole that was laying on the ground, he spun the pole like a staff and knocked two agents to the floor, creating an opening. He ran through the opening before throwing the pole at the rest of the agents knocking them all down. Next, he ran down the hall and went through another door and up the stairs to the third floor. On the third floor there was no one there, but the hall was full of traps and automated weapons. Chuck cartwheeled over a pit in the ground and then jump from the ground and bounced off the walls to avoid a laser and a stream of bullets. Chuck grabbed a small pebble from the ground and pen out of his pocket and threw them at the gun and laser. The pebble destroyed the laser system while the pencil clogged the gun; Chuck ran down the hallway and sprinted up the stairs to the desert resort at top of the stairs.

"This is the last level; this is going to be a breeze." Chuck said as he confidently walked onto the beach.

Suddenly from under the water, a special ops team appeared and then Chuck was surrounded by the team. Chuck looked at his fist and, using the Intersect, flashed. He suddenly went all berserk and roundhouse kicked, flipped, elbowed, punched, and totally demolished the special ops team. Chuck ran to the elevator and hit the up button. He got out of the elevator and ran to the door down the hall. When he opened the door, he saw General Beckman, Director Graham, and Agents Sigma and X waiting for him.

"Congratulations Mister Bartowski, you are now a fully certified agent of the CIA and NSA, here's your credentials and badge. Oh and I think it's time that you learned the real names of your teachers. Agent Sigma's name is Hongxiang Cai, a top spy of the Chinese Intelligence Agency until he defected, and LouieDean Natividad, a top spy of the Philippines that defected after an uncovering of some nasty business." General Beckman said.

AN:  
I hope you liked it!  
Please Review! I really need feedback so that I can improve my writing for all my readers.  
Thank you for reading!  
Dragonslayer9907 signing out.


	2. Chuck versus the Buy More

Dragonslayer9907 signing in.

And due to a very thoughtful review, I decided to add a few things into this chapter. I hope you like it.

Disclaimer: I don't own anything, because if I did I probably wouldn't be writing here.

Chuck versus the Buy More

"Oh and one more thing before you go Chuck. We would like you to know that you own the Burbank Buy More and a small cover computer business. Happy Holidays, Chuck! You're going to be home for Christmas." Beckman said.

"Woah, woah, woah! Did you just say that you gave me the Buy More and a computer business?" asked Chuck incredulously.

"Yes, that's what I said. I don't joke Bartowski. Who the hell do you think I am? I'm a soldier and the person in charge of the freaking Intersect Project, and we spies don't kid around." Beckman said forcefully.

"Thank you! Thank You! THANK YOU! I own the Buy More and Carmichael Industries! Ellie's going to be so happy that I have moved on in life! Oh right, where are the agents going to live?" Chuck yelled excitedly.

"Oh, that's not a problem Louie and I will be living in Castle." Sigma(Hongxiang) explained.

"What's Castle?" Chuck asked perplexed.

"Oh! Haha! I forgot you didn't know. The CIA and NSA used a lot of money to trick out the space under the Buy More into a completely equipped spy bunker." Sigma(Hongxiang) said.

"Ok enough of this crap! We're on a schedule here! Soldiers Move OUT!" General Beckman yelled.

"YES MA'AM!" everyone said as they boarded a chopper that was bound for Burbank.

/  
The group arrived at the Burbank Buy More and when Chuck walked in, the store went crazy.

"Chuck! How was it? What was it like in China? How much Chinese did you learn? Are you going to be staying here? How was the job? Was it hard?..." Everyone asked as they stormed Chuck.

"Woah! WOAH! WOAH! Calm down everyone. I'm here to stay for now I guess, but really why do you guys look like you just went to hell and came back?" Chuck asked.

"We need your help Chuck! Big Mike found a new Assistant Manager and well he became the Manager after a certain inspection and then he created a new Buy More. I mean even Jeff and Lester listen to him as if he's a god or something. Save us Chuck! Save us!" Morgan explained.

"Ummm... Yeah I'll talk to him later, I need to..." Chuck said as he looked for Louie and Eric (Hongxiang), "Oh never mind, wait is that him coming from the electronics section?" Chuck asked as Emmett walked toward the group to see what was causing all that ruckus.

"What do we have here? What is this? Who are you and what do you think you're doing? Are you trying to start a revolution? Security! Take him down!" asked Emmett as he looked at Chuck with a glare.

"Hi, I'm Chuck and I would like to have a little talk with you, if you have time that is." Chuck said as he knocked out the security guards with a hit to the back of the neck.

"Ummm... Wh...whhh...whhhaaaa...whhhaaaaatttttt dddddoooooo you waaannt to taaaalk abbbboooouttt?" Emmett asked while stuttering due to Chuck nonchalant expression as he knocked out the security guards.

"I would like to notify the Burbank Buy More that they have a new owner, Me. And I would appreciate it if my employees weren't robots in their everyday lives at the Buy More, we need to have emotions people!" Chuck said smiling. "Oh I won't be around to inspect this place often, as I need to attend to my business, but I am putting Morgan Grimes in charge of telling me if anything goes wrong, GOT IT?"

"Y...ye...yess... offffff cccouuurrsssee." Emmett whimpered as he almost peed his pants in fear.

"Good! Have a nice day and I'm going to slip into the break room for a small snack." Chuck said as he left for the break room.

"Yes! Party!" everyone but Emmett yelled as they ran around the store cheering.

In the breakroom

Chuck walked into the break room and grabbed a pack of Flaming Hot Munchies before looking around the room for the entrance to Castle. Chuck starting knocking on the lockers and was able to find the entrance hidden behind Casey's locker. Chuck moved the lockers aside and went down to Castle. When he got into Castle he found Louie and Eric(Hongxiang/Sigma) messing around with some of the computers in Castle.

Chuck set his stuff down behind them before walking into the training room. He started off with a thousand push-up and sit-up set before moving on to a thousand pull-ups. Then he picked up some throwing knives and starting throwing them at moving targets getting bullseyes every time. Chuck was so concentrated on his exercises that he didn't notice that Sarah had walked in and was watching him go through his exercises.

"I see that you have improved a lot in your field skills." Sarah stated from the door as she walked in.

"Oh hey Sarah! That's expected when you train with the two best agents of the CIA and NSA." Chuck said.

"So who are the two new people out there and why is Casey suddenly calling them "Sensei" and bowing to them as if they are gods or something?" Sarah asked intrigued.

"Oh! I forgot about them. Their names are Louie and Eric and well you probably know them Sigma and X. They took six months and turn me from the old Chuck into the new Chuck, but I would like you to know that I still find it hard to kill people and I still have my emotions." Chuck said.

"Wait! Hold up! Did you just say that the two people outside are the fabled Agents Sigma and X? The ones that don't go on missions anymore because their too destructive on some missions? The ones that trained almost every agent in both agencies? The ones that are pretty much the idol of every spy in the world? The ones that never failed a mission?" Sarah asked rapidly causing Chuck to be a little confused.

"Yeah, I think so." Chuck said.

"Anyway, away from that topic, mind if I join you?" Sarah asked as she picked up some knives.

"No not at all. Come let's see who gets the most bullseyes!" Chuck said.

Chuck and Sarah spent the rest of the day in the training arena sparring, working on aim, competing, and talking.

"Hey Sarah! Not bad!" Chuck said as Sarah got one more bullseye than he did. "Let's go to stars next."

"Chuck, how did you become so good in such a short time? I didn't think that you would be able to become such a good weapons master! I wonder if it's in your genes or something?" Sarah asked as she reset the targets and picked up some stars.

"Well, it was hard work and all and there were times when I wanted to quit and become the loser I was once more. But then I thought about how that if I didn't get stronger, get better, turn from a loser into a protector, then I would never be able to protect the people around me that I love and care about. That's what kept me going." Chuck said while looking Sarah in the eyes.

Flashback

Chuck was running around in the training room pushing himself to run the twenty warm-up laps that his new teachers wanted him to do. He wiped the sweat from his hairline and then he almost started to stop and but suddenly a picture of Sarah, Ellie, Awesome and Morgan popped into his mind and suddenly he felt revitalized. He starting training with a whole new vigor and decided to try his hardest to become the best spy that he could so that he could protect the people that he loved.

"How are you doing? You ready for what's next? After the run you have to do five hundred push-ups, sit-ups and pull-ups. Then you must be ready for a few hours of intense sparring and weapons training before venturing into the spy training." said Sigma before he walked out of the training room to the kitchen for a snack.

"No I'm fine! Thanks for asking!" Chuck yelled after the retreating back of Sigma.

Flashback End

"So Sarah are you ready to be beaten by the Master in throwing stars?" Chuck said as he grabbed a few stars and tossed them in the air experimentally.

"In your dreams Chuck, in your dreams!" Sarah said as she started throwing her stars at the targets in a rapid succession. Chuck and Sarah started to throw the stars at the targets rapidly and they were laughing and talking friendly. They continued to throw the stars at the targets pretty much always throwing bullseyes until Chuck decided to spice it up a little and bounce his star off of Sarah, effectively knocking it off course and into the outer ring of the target, and getting a bullseye.

"Hey that's not fair! That's sabotage Chuck!" Sarah complained.

"Sarah, we're spies. We use everything necessary to finish our missions, or in this case winning at this friendly competition." Chuck said jokingly.

"Okay fine Chuck after this let's play a game of target practice." Sarah said mysteriously.

"Sure how do we play?" Chuck asked as he threw his last throwing star at the target.

"I have a tranquilizer gun and well you're the Target!" Sarah said as she grab a tranq gun and started shooting tranq darts at Chuck.

After a while of running around and dodging darts, Chuck suddenly yelled, "Oh my Goodness! I forgot to get Ellie, you and everyone else Christmas presents. Oh and Sarah you're invited to the annual Bartowski Christmas party. Gotta Run!"

Chuck ran out of Castle and went around looking for the right presents for everyone before it was too late.

AN:  
Thus ends the second chapter. Will get more action packed and get a little more interesting later on. :)  
I hope you liked it!  
Please Review! I really need feedback so that I can improve my writing for all my readers.  
Thank you for reading!  
Dragonslayer9907 signing out.


	3. Chuck versus the Christmas Time Horrors

Dragonslayer9907 signing in.

AN: Christmas and happiness, funny how it's actually the fourth of July.

Disclaimer: I don't own anything, because if I did I probably wouldn't be writing here.

Chuck vs Christmas Time Horrors

The Buy More, a calm serene place where people of all ages bustled around looking for the right Christmas gifts. Discounts on everything, people working in harmony and effectively. The walls filled to the brim with the newest electronics, food, toys and appliances. Everything was going smoothly, until suddenly someone broke the harmony and peace of the store. Someone zoomed in, leaving dust in flying in his rush. Chuck Bartowski was his name and he was a man on a mission.

Chuck raced into the Buy More, searching for the right gifts for everyone. Zooming around the store, Chuck grabbed a 7G iPhone for Sarah, a 62" plasma screen TV for Ellie, a new MW3 game for Morgan, and got a washer/ dryer set for Devon. He ran to the register to pay for everything before going to the wrapping station to get everything wrapped.

"Will that be all, Chuck?" the person working the register asked.

"Yup, thanks a lot. Christmas is in two days and I need to go hide these presents. The washer, dryer, and TV are going to make it to the apartment on time right?" Chuck asked.

"Of course, you can count on us. We never let a comrade in arms down!" the cashier said as he passed Chuck the wrapped gifts and the tag for the appliances.

"Thanks, gotta go and freshen up my new house! I'll invite everyone for a housewarming party later." Chuck said as he rushed out the door.

At Chuck's new house

Chuck opened the door and walked into his new home. Everything was perfect, a little too perfect and classy. There were two staircases in across from the front door that led upstairs, a crystal chandelier lit up the open space between the front door and the arches that led to the living and dining rooms. There was a sliding panel on the wall next to the staircase that opened up to a cache of weapons. In the living room was filled with the finest furniture in the world. Plush sofas, comfy armchairs, a romantic loveseat and a nice little coffee table. But none of it was really what it seemed to be; the armchair was really a remote control to the missile security of the house, the sofas were sofas with a multitude of weapons under the cushions, the table had a sliding top that opened up to a government issue touchpad computer system, and the loveseat, well it really was a loveseat.

The dining room had a state of the art bar, a new refrigerator, a conventional oven, microwave, stove, sinks, cabinets and a pantry. The pantry had a fake wall and trap door inside it. The wall led to a secure office that was to be used in times of emergency and the trap door led to an underground tunnel system that led out of the house.

Upstairs there were all the bedrooms and the main office that was used to communications. The master bedroom had a California King sized bed and a dresser, even his old Tron poster was on the wall. The bathroom was amazing, complete with a spa, jacuzzi, and shower. Out back there was a 12ft deep pool, a grassy area, a spa area, a grill area, and a covered patio.

Chuck went up the stairs and hid the presents in the master bedroom before heading into the main office for a video conference with General Beckman. Chuck turned on the screen and politely saluted the General and Director.

"General, Director, what is my mission?" Chuck asked as he sat down in front of the screen.

"Agent Bartowski, there has been a report of Fulcrum agents in Sacramento, California and they seem to be planning something. We know that they have the Cipher for the new evolution of the Intersect. We believe that they are trying to create an Intersect that is going to be more powerful than the Intersect 2.0. This could mean trouble and your mission is to retrieve the Cipher at all costs. Your mission starts now. I don't know how long it will take. It may take a day or a week or maybe even a month." General Beckman said.

"But, General, no disrespect and all, Christmas is in two days and I can't miss out on Christmas or Ellie will kill me." Chuck said in complaint.

"Agent Bartowski! This mission is very important and if you don't succeed you may not have a very cheerful Christmas, so I advise you to push Christmas plans to the back of your mind and focus on the mission. Go and assemble your team." General Beckman reprimanded.

"Yes MA'AM!" Chuck said as he saluted before turning off the screen and walking out of the room to get ready for the mission.

Twenty minutes later at Castle

"Everybody gear up! We're going to the capital city for a little hunting expedition!" Chuck yelled as Casey, Sarah and the two elite agents went to the armory.

"So Chuck what guns do you plan to use?" Sarah asked as she grabbed a few rifles and pistols.

"HUH? Oh, just a tranq, killing people is a last resort and I don't need guns to kill people, a pencil will work too. This is going to be a simple mission and I hope that we can get back before Christmas or I'm really dead. Oh by the way, are you going to come to the party? Everyone's invited, of course." Chuck answered.

The team left Castle and drove to the airport before getting on a jet for Sacramento. Not long after landing and a little recon, they found the Fulcrum base.

In Sacramento, Fulcrum Base, Christmas Eve, 8:00 pm

"Okay team, the schematics of the base are pretty simple, two floors. The room that we need to get to is on the second floor in the far right corner. We're going to need someone to clear the first floor. Agents Sigma and X, I'll leave that to you. Casey, Sarah and I will be going straight for the second floor. Casey sweep the floor, Sarah and I will get the Cipher. Understood?" Chuck commanded.

"Understood!" everyone said simultaneously.

"Okay team, MOVE OUT!" Chuck commanded.

Agents Sigma and X swiftly entered the building and started to systematically sweep the first floor. They each took a corridor and with pinpoint accuracy shot everyone that they saw. They drew the attention of all of the guards that were on the first floor.

"All clear, Captain you are clear. Advance at will, sir." Agent Sigma said into a walkie talkie as X took out the last guard on the first floor.

Chuck and the others ran into the building before going up the stairs carefully. Once on the second floor, Casey split up with Chuck and Sarah. Casey went down the halls, shooting at everything and everyone trying to draw as much attention as possible. Almost every guard on the second floor ran toward the commotion that Casey was causing, while Chuck and Sarah quietly slipped down the hallway to the room in question. They stealthily ran down the halls taking out anyone that got in their way. When they got to the room, they broke the keypad off the wall and attached the government issued code breaker to the wiring. After a few minutes the code breaker cracked the code and the door opened. They slipped into the room and were about to start the search for the Cipher when they saw something that took the breath away from them.

AN:

This is the end of this lovely chapter.

I hope you liked it.

Please review!

Thanks for reading!

Dragonslayer9907 signing out.


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